Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002569.1 Hibiscus syriacus cultivar Beakdansim tig00005212_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 68681
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:361 original size:30 final size:32
Alignment explanation
Indices: 297--382 Score: 88
Period size: 32 Copynumber: 2.8 Consensus size: 32
287 AGTCGAGGGT
* * * *
297 TTACCTATGTTCTATGGA-ACATATTGACATAA
1 TTACCTATG-TCTTTCGAGACATATAGACAGAA
*
329 TTA-C-ATGTCTTTCGGGACATATAGACAGAA
1 TTACCTATGTCTTTCGAGACATATAGACAGAA
*
359 TTACCTATGTCTTTCTAGACATAT
1 TTACCTATGTCTTTCGAGACATAT
383 TGATAGTATA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
29 5 0.11
30 18 0.41
31 2 0.05
32 19 0.43
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.37
Consensus pattern (32 bp):
TTACCTATGTCTTTCGAGACATATAGACAGAA
Found at i:2003 original size:2 final size:2
Alignment explanation
Indices: 1996--2049 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1986 GTTAACCAAG
1996 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2038 TC TC TC TC TC TC
1 TC TC TC TC TC TC
2050 ATATCTGAGT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:11962 original size:34 final size:36
Alignment explanation
Indices: 11919--11986 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
11909 TTCATTTAGG
11919 GGGGAATCGATA-CCCCCA-GGGGGAATCTGTTCTC
1 GGGGAATCGATATCCCCCAGGGGGGAATCTGTTCTC
11953 GGGGAATCGATATCCCCCAGGGGGGAATCTGTTC
1 GGGGAATCGATATCCCCCAGGGGGGAATCTGTTC
11987 CCCCTGCACA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
34 12 0.38
35 6 0.19
36 14 0.44
ACGTcount: A:0.21, C:0.25, G:0.34, T:0.21
Consensus pattern (36 bp):
GGGGAATCGATATCCCCCAGGGGGGAATCTGTTCTC
Found at i:15301 original size:2 final size:2
Alignment explanation
Indices: 15294--15342 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
15284 AATCAATTAT
15294 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15336 TA TA TA T
1 TA TA TA T
15343 TCCAATGATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18061 original size:35 final size:36
Alignment explanation
Indices: 18009--18078 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 36
17999 TTCATTTAGG
*
18009 GGGGAATCGATACCCCCCA-GGGGGAATCTGTTCCA
1 GGGGAATCCATACCCCCCAGGGGGGAATCTGTTCCA
*
18044 GGGGAATCCATATCCCCCAGGGGGGAATCTGTTCC
1 GGGGAATCCATACCCCCCAGGGGGGAATCTGTTCC
18079 CCCCTGCACA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 17 0.53
36 15 0.47
ACGTcount: A:0.21, C:0.29, G:0.31, T:0.19
Consensus pattern (36 bp):
GGGGAATCCATACCCCCCAGGGGGGAATCTGTTCCA
Found at i:24759 original size:4 final size:4
Alignment explanation
Indices: 24750--25040 Score: 573
Period size: 4 Copynumber: 72.8 Consensus size: 4
24740 GATGTATATT
24750 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
24798 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
24846 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
24894 ATAC ATAC ATAC ATAT ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
24942 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
24990 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
25038 ATA
1 ATA
25041 AGTAGTAGTA
Statistics
Matches: 285, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
4 285 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:34193 original size:23 final size:23
Alignment explanation
Indices: 34167--34299 Score: 167
Period size: 23 Copynumber: 5.7 Consensus size: 23
34157 ACTTCTGTGC
* * *
34167 TGAATCATTTAACACTGTTTTAT
1 TGAATCAATCAACACTGTTTTGT
* *
34190 TGAATCAGTCAATACTGTTTTGT
1 TGAATCAATCAACACTGTTTTGT
*
34213 TGAATTAATCAACACTGTTTTGT
1 TGAATCAATCAACACTGTTTTGT
*
34236 TGAATTAATCAAACACTGTTTTGT
1 TGAATCAATC-AACACTGTTTTGT
*
34260 TGAATCAATCAACACTGTTTTAT
1 TGAATCAATCAACACTGTTTTGT
* *
34283 TGAATCAGTCAGCACTG
1 TGAATCAATCAACACTG
34300 AATCATTCAG
Statistics
Matches: 98, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
23 76 0.78
24 22 0.22
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.41
Consensus pattern (23 bp):
TGAATCAATCAACACTGTTTTGT
Found at i:34270 original size:47 final size:46
Alignment explanation
Indices: 34167--34299 Score: 176
Period size: 47 Copynumber: 2.9 Consensus size: 46
34157 ACTTCTGTGC
* * * *
34167 TGAATCATTTAACACTGTTTTATTGAATCAGTCAATACTGTTTTGT
1 TGAATCAATCAACACTGTTTTATTGAATCAATCAACACTGTTTTGT
* * *
34213 TGAATTAATCAACACTGTTTTGTTGAATTAATCAAACACTGTTTTGT
1 TGAATCAATCAACACTGTTTTATTGAATCAATC-AACACTGTTTTGT
* *
34260 TGAATCAATCAACACTGTTTTATTGAATCAGTCAGCACTG
1 TGAATCAATCAACACTGTTTTATTGAATCAATCAACACTG
34300 AATCATTCAG
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
46 33 0.45
47 41 0.55
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.41
Consensus pattern (46 bp):
TGAATCAATCAACACTGTTTTATTGAATCAATCAACACTGTTTTGT
Found at i:35152 original size:17 final size:17
Alignment explanation
Indices: 35109--35143 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
35099 CTTAGGAGGA
35109 AAAGAGGAGAGGAGGGG
1 AAAGAGGAGAGGAGGGG
35126 AAAGAGGAGAGGAGGGG
1 AAAGAGGAGAGGAGGGG
35143 A
1 A
35144 GAGTGGAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (17 bp):
AAAGAGGAGAGGAGGGG
Found at i:44124 original size:3 final size:3
Alignment explanation
Indices: 44116--44207 Score: 100
Period size: 3 Copynumber: 30.7 Consensus size: 3
44106 AGTTTGCATA
* * *
44116 TAT TAT TAT TAT TAC TA- TAT TAT TA- TAG TAT TAC TAT TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
*
44160 TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT TAA TA- TATT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TA-T TAT TAT
44206 TA
1 TA
44208 CAAATAATAC
Statistics
Matches: 78, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
2 6 0.08
3 64 0.82
4 8 0.10
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:44156 original size:28 final size:27
Alignment explanation
Indices: 44116--44207 Score: 109
Period size: 28 Copynumber: 3.4 Consensus size: 27
44106 AGTTTGCATA
44116 TATTATTATTATTACTATATTATTATAG
1 TATTATTATTATTA-TATATTATTATAG
* *
44144 TATTACTATTATT-TATTATTATTATTAT
1 TATTATTATTATTATA-TATTATTA-TAG
*
44172 TATTATTATTATTATATATTAATATA-
1 TATTATTATTATTATATATTATTATAG
44198 T-TTATTATTA
1 TATTATTATTA
44208 CAAATAATAC
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
25 9 0.16
26 3 0.05
27 10 0.18
28 33 0.58
29 2 0.04
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.61
Consensus pattern (27 bp):
TATTATTATTATTATATATTATTATAG
Found at i:44681 original size:3 final size:3
Alignment explanation
Indices: 44673--44755 Score: 73
Period size: 3 Copynumber: 27.7 Consensus size: 3
44663 AGTTTGCATA
* * *
44673 TAT TAT TAT TAT TAC TA- TAT TAT TA- TAG TAT TAC TAT TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
* *
44717 TAT TAC TAT TAT TAT TAT ATAT TAA TAT GT-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT -TAT TAT TAT TA
44756 CAAATAATAC
Statistics
Matches: 66, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
2 5 0.08
3 54 0.82
4 7 0.11
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:44750 original size:19 final size:17
Alignment explanation
Indices: 44675--44755 Score: 83
Period size: 19 Copynumber: 4.5 Consensus size: 17
44665 TTTGCATATA
*
44675 TTATTATTATTACTATA
1 TTATTATTATTACTATT
44692 TTATTATAGTATTACTATT
1 TTATTAT--TATTACTATT
*
44711 AT-TTATTATTACTATT
1 TTATTATTATTACTATT
*
44727 ATTATTATATATTAATATGT
1 -TTATTAT-TATTACTAT-T
44747 TTATTATTA
1 TTATTATTA
44756 CAAATAATAC
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
16 10 0.19
17 8 0.15
18 10 0.19
19 25 0.46
20 1 0.02
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (17 bp):
TTATTATTATTACTATT
Found at i:44750 original size:22 final size:22
Alignment explanation
Indices: 44678--44755 Score: 77
Period size: 22 Copynumber: 3.4 Consensus size: 22
44668 GCATATATTA
44678 TTATTATTACTATATTATTATAGT
1 TTATTATTA-TATATTATTAT-GT
* * *
44702 ATTACTATTATTTATTATTACT-A
1 -TTATTATTATATATTATTA-TGT
*
44725 TTATTATTATATATTAATATGT
1 TTATTATTATATATTATTATGT
44747 TTATTATTA
1 TTATTATTA
44756 CAAATAATAC
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
21 1 0.02
22 25 0.57
24 9 0.20
25 9 0.20
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.59
Consensus pattern (22 bp):
TTATTATTATATATTATTATGT
Found at i:46781 original size:21 final size:21
Alignment explanation
Indices: 46752--46809 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
46742 GGGACTACGC
* *
46752 GATCCTTCGGGACAACTT-ATA
1 GATCATTCGGGACAA-TTCACA
46773 GATCATTCGGGACATATTCACA
1 GATCATTCGGGACA-ATTCACA
*
46795 GGTCATTCGGGACAA
1 GATCATTCGGGACAA
46810 AATTTCATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 16 0.50
22 16 0.50
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (21 bp):
GATCATTCGGGACAATTCACA
Found at i:47889 original size:40 final size:40
Alignment explanation
Indices: 47780--47889 Score: 118
Period size: 40 Copynumber: 2.8 Consensus size: 40
47770 GGATGTTAAA
*
47780 ACTCACATCAACAAGAAGAAAATGTTGGGGCATTTTGAAG
1 ACTCACATTAACAAGAAGAAAATGTTGGGGCATTTTGAAG
* * *
47820 AC-C-CATTCCAACCAGAATTAGAATG-TGGGGCATTTTGAAG
1 ACTCACATT--AACAAGAA-GAAAATGTTGGGGCATTTTGAAG
* *
47860 ACTCACATTAACAAGAAGCAAACGTTGGGG
1 ACTCACATTAACAAGAAGAAAATGTTGGGG
47890 TATGCTGAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
38 3 0.05
39 4 0.07
40 38 0.69
41 6 0.11
42 4 0.07
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (40 bp):
ACTCACATTAACAAGAAGAAAATGTTGGGGCATTTTGAAG
Found at i:52612 original size:24 final size:24
Alignment explanation
Indices: 52583--52630 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
52573 TTTTCATTTG
*
52583 GTCATTCCATGCATAATTTAAACA
1 GTCATTCAATGCATAATTTAAACA
52607 GTCATTCAATGCATAATTTAAACA
1 GTCATTCAATGCATAATTTAAACA
52631 ACTTTTCAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (24 bp):
GTCATTCAATGCATAATTTAAACA
Found at i:54009 original size:13 final size:13
Alignment explanation
Indices: 53987--54031 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
53977 AATAAAAATA
53987 TAAAAATATATTT
1 TAAAAATATATTT
* *
54000 TAAAATTATATAT
1 TAAAAATATATTT
54013 TAAAAATAT-TTT
1 TAAAAATATATTT
*
54025 TATAAAT
1 TAAAAAT
54032 TAAATATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 8 0.30
13 19 0.70
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TAAAAATATATTT
Found at i:54020 original size:26 final size:26
Alignment explanation
Indices: 53982--54039 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
53972 ACTATAATAA
53982 AAATA-TAAAAATATATTTTA-AAATT
1 AAATATTAAAAATAT-TTTTATAAATT
*
54007 ATATATTAAAAATATTTTTATAAATT
1 AAATATTAAAAATATTTTTATAAATT
54033 AAATATT
1 AAATATT
54040 TTATTAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 9 0.31
26 20 0.69
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
AAATATTAAAAATATTTTTATAAATT
Found at i:58461 original size:3 final size:3
Alignment explanation
Indices: 58453--58524 Score: 144
Period size: 3 Copynumber: 24.0 Consensus size: 3
58443 AATGGTATGG
58453 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
58501 ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA
58525 TGGATAAATG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:58749 original size:6 final size:6
Alignment explanation
Indices: 58740--58827 Score: 176
Period size: 6 Copynumber: 14.7 Consensus size: 6
58730 CATCATCGTC
58740 ATAACA ATAACA ATAACA ATAACA ATAACA ATAACA ATAACA ATAACA
1 ATAACA ATAACA ATAACA ATAACA ATAACA ATAACA ATAACA ATAACA
58788 ATAACA ATAACA ATAACA ATAACA ATAACA ATAACA ATAA
1 ATAACA ATAACA ATAACA ATAACA ATAACA ATAACA ATAA
58828 TAATTCGATG
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 82 1.00
ACGTcount: A:0.67, C:0.16, G:0.00, T:0.17
Consensus pattern (6 bp):
ATAACA
Found at i:62640 original size:24 final size:24
Alignment explanation
Indices: 62613--62659 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
62603 TCTTCTCAAC
* *
62613 AAGAACAATTTGTCTCTGCTGAGT
1 AAGAACAATCTGTCTCTACTGAGT
* *
62637 AAGATCAGTCTGTCTCTACTGAG
1 AAGAACAATCTGTCTCTACTGAG
62660 CATGTTCAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (24 bp):
AAGAACAATCTGTCTCTACTGAGT
Found at i:68073 original size:23 final size:23
Alignment explanation
Indices: 68047--68113 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
68037 CACCACAGCT
*
68047 CGTATAATTGCACCGAAGTGCCG
1 CGTATAATTGCACCGAAGTGCCA
* * *
68070 CGTAGAAATGCACCGTAGTGCCA
1 CGTATAATTGCACCGAAGTGCCA
*
68093 CGTAT--TTACACCGAAGTGCCA
1 CGTATAATTGCACCGAAGTGCCA
68114 TATAAATGTC
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
21 13 0.36
23 23 0.64
ACGTcount: A:0.28, C:0.27, G:0.24, T:0.21
Consensus pattern (23 bp):
CGTATAATTGCACCGAAGTGCCA
Done.